| 1. |
- Blanton, Michael R., et al.
(författare)
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Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe
- 2017
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Ingår i: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1
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Tidskriftsartikel (refereegranskat)abstract
- We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
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| 2. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
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Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 3. |
- Brownstein, Catherine A., et al.
(författare)
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An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge
- 2014
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Ingår i: Genome Biology. - : Springer Science and Business Media LLC. - 1465-6906 .- 1474-760X. ; 15:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- Background: There is tremendous potential for genome sequencing to improve clinical diagnosis and care once it becomes routinely accessible, but this will require formalizing research methods into clinical best practices in the areas of sequence data generation, analysis, interpretation and reporting. The CLARITY Challenge was designed to spur convergence in methods for diagnosing genetic disease starting from clinical case history and genome sequencing data. DNA samples were obtained from three families with heritable genetic disorders and genomic sequence data were donated by sequencing platform vendors. The challenge was to analyze and interpret these data with the goals of identifying disease-causing variants and reporting the findings in a clinically useful format. Participating contestant groups were solicited broadly, and an independent panel of judges evaluated their performance. Results: A total of 30 international groups were engaged. The entries reveal a general convergence of practices on most elements of the analysis and interpretation process. However, even given this commonality of approach, only two groups identified the consensus candidate variants in all disease cases, demonstrating a need for consistent fine-tuning of the generally accepted methods. There was greater diversity of the final clinical report content and in the patient consenting process, demonstrating that these areas require additional exploration and standardization. Conclusions: The CLARITY Challenge provides a comprehensive assessment of current practices for using genome sequencing to diagnose and report genetic diseases. There is remarkable convergence in bioinformatic techniques, but medical interpretation and reporting are areas that require further development by many groups.
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| 4. |
- Chen, Zhishan, et al.
(författare)
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Fine-mapping analysis including over 254 000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes
- 2024
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 15:1
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV. Our cis-eQTL/mQTL and colocalization analyses using colorectal tissue-specific transcriptome and methylome data separately from 1299 and 321 individuals, along with functional genomic investigation, uncovered 136 putative CRC susceptibility genes, including 56 genes not previously reported. Analyses of single-cell RNA-seq data from colorectal tissues revealed 17 putative CRC susceptibility genes with distinct expression patterns in specific cell types. Analyses of whole exome sequencing data provided additional support for several target genes identified in this study as CRC susceptibility genes. Enrichment analyses of the 136 genes uncover pathways not previously linked to CRC risk. Our study substantially expanded association signals for CRC and provided additional insight into the biological mechanisms underlying CRC development.
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| 5. |
- Dai, Qile, et al.
(författare)
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OTTERS: a powerful TWAS framework leveraging summary-level reference data
- 2023
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 14:1
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Tidskriftsartikel (refereegranskat)abstract
- Most existing TWAS tools require individual-level eQTL reference data and thus are not applicable to summary-level reference eQTL datasets. The development of TWAS methods that can harness summary-level reference data is valuable to enable TWAS in broader settings and enhance power due to increased reference sample size. Thus, we develop a TWAS framework called OTTERS (Omnibus Transcriptome Test using Expression Reference Summary data) that adapts multiple polygenic risk score (PRS) methods to estimate eQTL weights from summary-level eQTL reference data and conducts an omnibus TWAS. We show that OTTERS is a practical and powerful TWAS tool by both simulations and application studies.
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| 6. |
- Koelmel, Jeremy P., et al.
(författare)
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An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry
- 2022
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Ingår i: Exposome. - : Oxford University Press. - 2635-2265 .- 2635-2265. ; 2:1
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Tidskriftsartikel (refereegranskat)abstract
- Omics-based technologies have enabled comprehensive characterization of our exposure to environmental chemicals (chemical exposome) as well as assessment of the corresponding biological responses at the molecular level (eg, metabolome, lipidome, proteome, and genome). By systematically measuring personal exposures and linking these stimuli to biological perturbations, researchers can determine specific chemical exposures of concern, identify mechanisms and biomarkers of toxicity, and design interventions to reduce exposures. However, further advancement of metabolomics and exposomics approaches is limited by a lack of standardization and approaches for assigning confidence to chemical annotations. While a wealth of chemical data is generated by gas chromatography high-resolution mass spectrometry (GC-HRMS), incorporating GC-HRMS data into an annotation framework and communicating confidence in these assignments is challenging. It is essential to be able to compare chemical data for exposomics studies across platforms to build upon prior knowledge and advance the technology. Here, we discuss the major pieces of evidence provided by common GC-HRMS workflows, including retention time and retention index, electron ionization, positive chemical ionization, electron capture negative ionization, and atmospheric pressure chemical ionization spectral matching, molecular ion, accurate mass, isotopic patterns, database occurrence, and occurrence in blanks. We then provide a qualitative framework for incorporating these various lines of evidence for communicating confidence in GC-HRMS data by adapting the Schymanski scoring schema developed for reporting confidence levels by liquid chromatography HRMS (LC-HRMS). Validation of our framework is presented using standards spiked in plasma, and confident annotations in outdoor and indoor air samples, showing a false-positive rate of 12% for suspect screening for chemical identifications assigned as Level 2 (when structurally similar isomers are not considered false positives). This framework is easily adaptable to various workflows and provides a concise means to communicate confidence in annotations. Further validation, refinements, and adoption of this framework will ideally lead to harmonization across the field, helping to improve the quality and interpretability of compound annotations obtained in GC-HRMS.
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| 7. |
- Lin, Yuanyuan, et al.
(författare)
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Investigation of the Reynolds number independence of cavity flow in 2D street canyons by wind tunnel experiments and numerical simulations
- 2021
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Ingår i: Building and Environment. - : Elsevier. - 0360-1323 .- 1873-684X. ; 201
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Tidskriftsartikel (refereegranskat)abstract
- The Reynolds number independence (Re independence) criterion of Re > 11,000 is widely adopted to fulfill the dynamic similarity between the urban flow modeling and the down-scale measurements. However, for 2D street canyons with H/W ≥ 1.5, experiments, numerical simulations, and in-situ observations have reported different vortex-flow regimes with similar building configurations but at different scales. This study uses both wind tunnel experiments and numerical simulations to revisit the Re-independent flow regimes and Re independence criteria with an extensive Re range for idealized 2D street canyons with various aspect ratios (H/W = 1.1, 2.4, 3, 4, and 5). We introduced an optimized ratio of relative changes (RRCs) to evaluate the flow regimes’ similarity. The wind tunnel experiment confirms that the cavity flow with H/W = 1.1 meets the Re independence when reference building Re (Reref) exceeds 11,000. Simulations validated by the experiment results are conducted to investigate detailed flow regimes and the critical Re (Rec) range for each aspect ratio. The canyons with H/W = 2.4, 3, and 4 are dominated by a single asymmetric vortex when the Re independence is satisfied, while there are two vertically-stacked counter-rotating vortices in the canyon with H/W = 5. The value range of Rec increases with aspect ratio from 1.9 × 104–2.6 × 104 (H/W = 2.4) to 1.3 × 105–2.1 × 105 (H/W = 3), and 2.1 × 106–6.4 × 106 (H/W = 4 and 5). Our results indicate that the fully Re-independent flow regimes in deep canyons have fewer vortices than the literature value with down-scale experiments and simulations. The variant Rec with different aspect ratios suggests the requirement to conduct the Re-independence test for different model configurations.
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| 8. |
- Lin, Yingbo, et al.
(författare)
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SUMO-modified insulin-like growth factor 1 receptor (IGF-1R) increases cell cycle progression and cell proliferation
- 2017
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Ingår i: Journal of Cellular Physiology. - : John Wiley & Sons. - 0021-9541 .- 1097-4652. ; 232:10, s. 2722-2730
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Tidskriftsartikel (refereegranskat)abstract
- Increasing number of studies have shown nuclear localization of the insulin-like growth factor 1 receptor (nIGF-1R) in tumor cells and its links to adverse clinical outcome in various cancers. Any obvious cell physiological roles of nIGF-1R have, however, still not been disclosed. Previously, we reported that IGF-1R translocates to cell nucleus and modulates gene expression by binding to enhancers, provided that the receptor is SUMOylated. In this study, we constructed stable transfectants of wild type IGF1R (WT) and triple-SUMO-site-mutated IGF1R (TSM) using igf1r knockout mouse fibroblasts (R-). Cell clones (R-WT and R-TSM) expressing equal amounts of IGF1R were selected for experiments. Phosphorylation of IGF-1R, Akt, and Erk upon IGF-1 stimulation was equal in R-WT and R-TSM. WT was confirmed to enter nuclei. TSM did also undergo nuclear translocation, although to a lesser extent. This may be explained by that TSM heterodimerizes with insulin receptor, which is known to translocate to cell nuclei. R-WT proliferated substantially faster than R-TSM, which did not differ significantly from the empty vector control. Upon IGF-1 stimulationG1-S-phase progression of R-WT increased from 12 to 38%, compared to 13 to 20% of R-TSM. The G1-S progression of R-WT correlated with increased expression of cyclin D1, A, and CDK2, as well as downregulation of p27. This suggests that SUMO-IGF-1R affects upstream mechanisms that control and coordinate expression of cell cycle regulators. Further studies to identify such SUMO-IGF-1R dependent mechanisms seem important.
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| 9. |
- Xie, Shijie, et al.
(författare)
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A novel criterion for yield shear displacement of rock discontinuities based on renormalization group theory
- 2023
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Ingår i: Engineering Geology. - : Elsevier BV. - 0013-7952 .- 1872-6917. ; 314
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Tidskriftsartikel (refereegranskat)abstract
- Research on the plastic shear deformation of rock discontinuities is essential to the structural design of rock engineering, and the yield point is an important indicator for plastic shear deformation. In this paper, a con-ceptual model based on renormalization group theory is proposed to qualitatively explain the evolution mode of shear deformation. Then, considering the stress transfer mechanism, the mathematical description of the critical failure point is derived. Subsequently, the criterion for yield shear displacement is obtained by combining the renormalization group model with the shear constitutive model. Finally, experimental results based on the ratio of yield stress to shear strength for different rock types are provided to verify the proposed criterion. The theoretical and mathematical analysis indicates that the yield point is the phase transition point during the shear deformation of rock discontinuities, which is equivalent to the critical failure point in the renormalization group theory. The relationship between the failure probability of n-order blocks and the basic failure probability can be obtained according to the stress transfer mechanism and the conditional probability, so that a mathematical description of the critical failure point can be established. The verification by both laboratory and in-situ tests shows that the results of the proposed criterion are consistent with those of classical methods. In addition, the determination of the parameters has little influence on the criterion's performance, which means the proposed criterion could eliminate the subjectiveness in determining the yield shear displacement.
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| 10. |
- Xie, Shijie, et al.
(författare)
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Modeling description of interface shear deformation : A theoretical study on damage statistical distributions
- 2023
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Ingår i: Construction and Building Materials. - : Elsevier BV. - 0950-0618 .- 1879-0526. ; 394
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Tidskriftsartikel (refereegranskat)abstract
- The shear constitutive model is important for the analysis of the interface shear deformation mechanism. In this study, five statistical distributions, including four that have never been applied in interface shear deformation, are introduced to describe the damage evolution of the interface. The corresponding statistical damage constitutive models are developed, and they have been validated using a series of experimental data (both laboratory and in-situ tests) at the rock-concrete interface. The comparison results with laboratory data show that the Mitscherlich model has the lowest prediction accuracy. By comparing with in-situ data, the Weibull model shows the best-predicted performance. Based on the Akaike information criterion metric, the Morgan-Mercer-Flodin (MMF) model performs much better than the other models in the laboratory tests, which indicates the MMF model can be introduced for a comprehensive analysis of interface shear deformation. In addition, the similarities between the MMF model and the Weibull model are found through the canonical transformation of the MMF model. And the analysis of the two unknown parameters of the MMF model shows that they are related to the yield characteristics and strength characteristics of the interface, respectively. Based on the damage variable evolution, the shear deformation of the interface can be divided into three phases, i.e., damage initiation phase, damage acceleration phase and damage slowing phase. And the parameters of the MMF model have an important influence on the damage variable curves.
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